docs/changes/newsfragments/405.change

@@ -0,0 +1 @@
+``native_t1w`` parameter has been replaced with ``space`` to allow :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede Raimondo`_

docs/changes/newsfragments/405.enh

@@ -0,0 +1 @@
+Update :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede Raimondo`_

junifer/datagrabber/aomic/id1000.py

@@ -11,6 +11,7 @@ from pathlib import Path
 from typing import Union
 
 from ...api.decorators import register_datagrabber
+from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
@@ -31,8 +32,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
            "FreeSurfer"} or list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
-    native_t1w : bool, optional
+    space : {"native", "MNI152NLin2009cAsym"}, optional
-        Whether to use T1w in native space (default False).
+        The space to use for the data (default "MNI152NLin2009cAsym").
 
     """
 
@@ -40,25 +41,40 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         self,
         datadir: Union[str, Path, None] = None,
         types: Union[str, list[str], None] = None,
-        native_t1w: bool = False,
+        space: str = "MNI152NLin2009cAsym",
     ) -> None:
+        valid_spaces = ["native", "MNI152NLin2009cAsym"]
+        if space not in ["native", "MNI152NLin2009cAsym"]:
+            raise_error(
+                f"Invalid space {space}. Must be one of {valid_spaces}"
+            )
+
+        # Descriptor for space in `anat`
+        sp_anat_desc = (
+            "" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
+        # Descriptor for space in `func`
+        sp_func_desc = (
+            "space-T1w_" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
         # The patterns
         patterns = {
             "BOLD": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/func/"
                     "{subject}_task-moviewatching_"
-                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                    f"{sp_func_desc}"
+                    "desc-preproc_bold.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/func/"
                         "{subject}_task-moviewatching_"
-                        "space-MNI152NLin2009cAsym_"
+                        f"{sp_func_desc}"
                         "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
                 "confounds": {
                     "pattern": (
@@ -68,46 +84,59 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                     ),
                     "format": "fmriprep",
                 },
+                "reference": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/func/"
+                        "{subject}_task-moviewatching_"
+                        f"{sp_func_desc}"
+                        "boldref.nii.gz"
+                    ),
+                },
             },
             "T1w": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
                     "desc-preproc_T1w.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_"
+                        "{subject}_"
+                        f"{sp_anat_desc}"
                         "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
             },
             "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "CSF_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-CSF_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "GM_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-GM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "WM_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-WM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "DWI": {
                 "pattern": (
@@ -148,27 +177,6 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                     )
                 },
             },
-        }
-        # Use native T1w assets
-        self.native_t1w = False
-        if native_t1w:
-            self.native_t1w = True
-            patterns.update(
-                {
-                    "T1w": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_desc-preproc_T1w.nii.gz"
-                        ),
-                        "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_desc-brain_mask.nii.gz"
-                            ),
-                            "space": "native",
-                        },
-                    },
             "Warp": [
                 {
                     "pattern": (
@@ -192,7 +200,15 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 },
             ],
         }
-            )
+        if space == "native":
+            patterns["BOLD"]["prewarp_space"] = "MNI152NLin2009cAsym"
+
+        else:
+            patterns["BOLD"]["prewarp_space"] = "native"
+
+        # Use native T1w assets
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())

junifer/datagrabber/aomic/piop1.py

@@ -37,8 +37,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             "gstroop", "workingmemory"} or list of the options, optional
         AOMIC PIOP1 task sessions. If None, all available task sessions are
         selected (default None).
-    native_t1w : bool, optional
+    space : {"native", "MNI152NLin2009cAsym"}, optional
-        Whether to use T1w in native space (default False).
+        The space to use for the data (default "MNI152NLin2009cAsym").
 
     Raises
     ------
@@ -52,8 +52,13 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         datadir: Union[str, Path, None] = None,
         types: Union[str, list[str], None] = None,
         tasks: Union[str, list[str], None] = None,
-        native_t1w: bool = False,
+        space: str = "MNI152NLin2009cAsym",
     ) -> None:
+        valid_spaces = ["native", "MNI152NLin2009cAsym"]
+        if space not in ["native", "MNI152NLin2009cAsym"]:
+            raise_error(
+                f"Invalid space {space}. Must be one of {valid_spaces}"
+            )
         # Declare all tasks
         all_tasks = [
             "restingstate",
@@ -78,22 +83,32 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                         " dataset!"
                     )
         self.tasks = tasks
+        # Descriptor for space in `anat`
+        sp_anat_desc = (
+            "" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
+        # Descriptor for space in `func`
+        sp_func_desc = (
+            "space-T1w_" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
         # The patterns
         patterns = {
             "BOLD": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/func/"
                     "{subject}_task-{task}_"
-                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                    f"{sp_func_desc}"
+                    "desc-preproc_bold.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/func/"
                         "{subject}_task-{task}_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                        f"{sp_func_desc}"
+                        "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
                 "confounds": {
                     "pattern": (
@@ -103,46 +118,59 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     ),
                     "format": "fmriprep",
                 },
+                "reference": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/func/"
+                        "{subject}_task-{task}_"
+                        f"{sp_func_desc}"
+                        "boldref.nii.gz"
+                    ),
+                },
             },
             "T1w": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
                     "desc-preproc_T1w.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_"
+                        "{subject}_"
+                        f"{sp_anat_desc}"
                         "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
             },
             "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "CSF_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-CSF_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "GM_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-GM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "WM_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-WM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "DWI": {
                 "pattern": (
@@ -183,27 +211,6 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     )
                 },
             },
-        }
-        # Use native T1w assets
-        self.native_t1w = False
-        if native_t1w:
-            self.native_t1w = True
-            patterns.update(
-                {
-                    "T1w": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_desc-preproc_T1w.nii.gz"
-                        ),
-                        "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_desc-brain_mask.nii.gz"
-                            ),
-                            "space": "native",
-                        },
-                    },
             "Warp": [
                 {
                     "pattern": (
@@ -227,7 +234,15 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 },
             ],
         }
-            )
+
+        if space == "native":
+            patterns["BOLD"]["prewarp_space"] = "MNI152NLin2009cAsym"
+        else:
+            patterns["BOLD"]["prewarp_space"] = "native"
+
+        # Use native T1w assets
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())

junifer/datagrabber/aomic/piop2.py

@@ -37,8 +37,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             list of the options, optional
         AOMIC PIOP2 task sessions. If None, all available task sessions are
         selected (default None).
-    native_t1w : bool, optional
+    space : {"native", "MNI152NLin2009cAsym"}, optional
-        Whether to use T1w in native space (default False).
+        The space to use for the data (default "MNI152NLin2009cAsym").
 
     Raises
     ------
@@ -52,8 +52,13 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         datadir: Union[str, Path, None] = None,
         types: Union[str, list[str], None] = None,
         tasks: Union[str, list[str], None] = None,
-        native_t1w: bool = False,
+        space: str = "MNI152NLin2009cAsym",
     ) -> None:
+        valid_spaces = ["native", "MNI152NLin2009cAsym"]
+        if space not in ["native", "MNI152NLin2009cAsym"]:
+            raise_error(
+                f"Invalid space {space}. Must be one of {valid_spaces}"
+            )
         # Declare all tasks
         all_tasks = [
             "restingstate",
@@ -76,22 +81,32 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                         " dataset!"
                     )
         self.tasks = tasks
+        # Descriptor for space in `anat`
+        sp_anat_desc = (
+            "" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
+        # Descriptor for space in `func`
+        sp_func_desc = (
+            "space-T1w_" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
         # The patterns
         patterns = {
             "BOLD": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/func/"
                     "{subject}_task-{task}_"
-                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                    f"{sp_func_desc}"
+                    "desc-preproc_bold.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/func/"
                         "{subject}_task-{task}_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                        f"{sp_func_desc}"
+                        "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
                 "confounds": {
                     "pattern": (
@@ -101,46 +116,59 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     ),
                     "format": "fmriprep",
                 },
+                "reference": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/func/"
+                        "{subject}_task-{task}_"
+                        f"{sp_func_desc}"
+                        "boldref.nii.gz"
+                    ),
+                },
             },
             "T1w": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
                     "desc-preproc_T1w.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_"
+                        "{subject}_"
+                        f"{sp_anat_desc}"
                         "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
             },
             "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "CSF_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-CSF_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "GM_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-GM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "{subject}_"
-                    "WM_probseg.nii.gz"
+                    f"{sp_anat_desc}"
+                    "label-WM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "DWI": {
                 "pattern": (
@@ -181,27 +209,6 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     )
                 },
             },
-        }
-        # Use native T1w assets
-        self.native_t1w = False
-        if native_t1w:
-            self.native_t1w = True
-            patterns.update(
-                {
-                    "T1w": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_desc-preproc_T1w.nii.gz"
-                        ),
-                        "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_desc-brain_mask.nii.gz"
-                            ),
-                            "space": "native",
-                        },
-                    },
             "Warp": [
                 {
                     "pattern": (
@@ -225,7 +232,15 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 },
             ],
         }
-            )
+
+        if space == "native":
+            patterns["BOLD"]["prewarp_space"] = "MNI152NLin2009cAsym"
+        else:
+            patterns["BOLD"]["prewarp_space"] = "native"
+
+        # Use native T1w assets
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -18,20 +18,25 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types",
+    "type_, nested_types, space",
     [
-        ("BOLD", ["confounds", "mask"]),
+        ("BOLD", ["confounds", "mask", "reference"], "MNI152NLin2009cAsym"),
-        ("T1w", ["mask"]),
+        ("BOLD", ["confounds", "mask", "reference"], "native"),
-        ("VBM_CSF", None),
+        ("T1w", ["mask"], "MNI152NLin2009cAsym"),
-        ("VBM_GM", None),
+        ("T1w", ["mask"], "native"),
-        ("VBM_WM", None),
+        ("VBM_CSF", None, "MNI152NLin2009cAsym"),
-        ("DWI", None),
+        ("VBM_CSF", None, "native"),
-        ("FreeSurfer", None),
+        ("VBM_GM", None, "MNI152NLin2009cAsym"),
+        ("VBM_GM", None, "native"),
+        ("VBM_WM", None, "MNI152NLin2009cAsym"),
+        ("DWI", None, "MNI152NLin2009cAsym"),
+        ("FreeSurfer", None, "MNI152NLin2009cAsym"),
     ],
 )
 def test_DataladAOMICID1000(
     type_: str,
     nested_types: Optional[list[str]],
+    space: str,
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber.
 
@@ -41,9 +46,11 @@ def test_DataladAOMICID1000(
         The parametrized type.
     nested_types : list of str or None
         The parametrized nested types.
+    space: str
+        The parametrized space.
 
     """
-    dg = DataladAOMICID1000(types=type_)
+    dg = DataladAOMICID1000(types=type_, space=space)
     # Set URI to Gin
     dg.uri = URI
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -18,30 +18,62 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types, tasks",
+    "type_, nested_types, tasks, space",
     [
-        ("BOLD", ["confounds", "mask"], None),
-        ("BOLD", ["confounds", "mask"], ["anticipation"]),
-        ("BOLD", ["confounds", "mask"], ["emomatching", "faces"]),
-        ("BOLD", ["confounds", "mask"], ["restingstate"]),
-        ("BOLD", ["confounds", "mask"], ["workingmemory", "gstroop"]),
         (
             "BOLD",
-            ["confounds", "mask"],
+            ["confounds", "mask", "reference"],
-            ["anticipation", "faces", "restingstate"],
+            None,
+            "MNI152NLin2009cAsym",
         ),
-        ("T1w", ["mask"], None),
+        ("BOLD", ["confounds", "mask", "reference"], None, "native"),
-        ("VBM_CSF", None, None),
+        (
-        ("VBM_GM", None, None),
+            "BOLD",
-        ("VBM_WM", None, None),
+            ["confounds", "mask", "reference"],
-        ("DWI", None, None),
+            ["anticipation"],
-        ("FreeSurfer", None, None),
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["emomatching", "faces"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["restingstate"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["workingmemory", "gstroop"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["anticipation", "faces", "restingstate"],
+            "MNI152NLin2009cAsym",
+        ),
+        ("T1w", ["mask"], None, "MNI152NLin2009cAsym"),
+        ("T1w", ["mask"], None, "native"),
+        ("VBM_CSF", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_CSF", None, None, "native"),
+        ("VBM_GM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_GM", None, None, "native"),
+        ("VBM_WM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_WM", None, None, "native"),
+        ("DWI", None, None, "MNI152NLin2009cAsym"),
+        ("FreeSurfer", None, None, "MNI152NLin2009cAsym"),
     ],
 )
 def test_DataladAOMICPIOP1(
     type_: str,
     nested_types: Optional[list[str]],
     tasks: Optional[list[str]],
+    space: str,
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
@@ -53,9 +85,11 @@ def test_DataladAOMICPIOP1(
         The parametrized nested types.
     tasks : list of str or None
         The parametrized task values.
+    space: str
+        The parametrized space.
 
     """
-    dg = DataladAOMICPIOP1(types=type_, tasks=tasks)
+    dg = DataladAOMICPIOP1(types=type_, tasks=tasks, space=space)
     # Set URI to Gin
     dg.uri = URI
 

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -18,25 +18,56 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types, tasks",
+    "type_, nested_types, tasks, space",
     [
-        ("BOLD", ["confounds", "mask"], None),
+        (
-        ("BOLD", ["confounds", "mask"], ["restingstate"]),
+            "BOLD",
-        ("BOLD", ["confounds", "mask"], ["restingstate", "stopsignal"]),
+            ["confounds", "mask", "reference"],
-        ("BOLD", ["confounds", "mask"], ["workingmemory", "stopsignal"]),
+            None,
-        ("BOLD", ["confounds", "mask"], ["workingmemory"]),
+            "MNI152NLin2009cAsym",
-        ("T1w", ["mask"], None),
+        ),
-        ("VBM_CSF", None, None),
+        ("BOLD", ["confounds", "mask", "reference"], None, "native"),
-        ("VBM_GM", None, None),
+        (
-        ("VBM_WM", None, None),
+            "BOLD",
-        ("DWI", None, None),
+            ["confounds", "mask", "reference"],
-        ("FreeSurfer", None, None),
+            ["restingstate"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["restingstate", "stopsignal"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["workingmemory", "stopsignal"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["workingmemory"],
+            "MNI152NLin2009cAsym",
+        ),
+        ("T1w", ["mask"], None, "MNI152NLin2009cAsym"),
+        ("T1w", ["mask"], None, "native"),
+        ("VBM_CSF", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_CSF", None, None, "native"),
+        ("VBM_GM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_GM", None, None, "native"),
+        ("VBM_WM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_WM", None, None, "native"),
+        ("DWI", None, None, "MNI152NLin2009cAsym"),
+        ("FreeSurfer", None, None, "MNI152NLin2009cAsym"),
     ],
 )
 def test_DataladAOMICPIOP2(
     type_: str,
     nested_types: Optional[list[str]],
     tasks: Optional[list[str]],
+    space: str,
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber.
 
@@ -48,9 +79,11 @@ def test_DataladAOMICPIOP2(
         The parametrized nested types.
     tasks : list of str or None
         The parametrized task values.
+    space: str
+        The parametrized space.
 
     """
-    dg = DataladAOMICPIOP2(types=type_, tasks=tasks)
+    dg = DataladAOMICPIOP2(types=type_, tasks=tasks, space=space)
     # Set URI to Gin
     dg.uri = URI
 

tools/create_aomic1000_example_dataset.py

@@ -4,6 +4,7 @@
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
 #          Xuan Li <xu.li@fz-juelich.de>
 # License: AGPL
+
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -39,30 +40,70 @@ with TemporaryDirectory() as tmpdir_name:
                     (sub_dir / dname).mkdir()
 
                 fnames = [
+                    # T1w native
+                    f"anat/{t_sub}_desc-preproc_T1w.nii.gz",
+                    # T1w MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_desc-preproc"
                         "_T1w.nii.gz"
                     ),
+                    # T1w brain mask native
+                    f"anat/{t_sub}_desc-brain_mask.nii.gz",
+                    # T1w brain mask MNI152NLin2009cAsym
+                    (
+                        f"anat/{t_sub}_space-MNI152NLin2009cAsym_"
+                        "desc-brain_mask.nii.gz"
+                    ),
+                    # CSF native
+                    f"anat/{t_sub}_label-CSF_probseg.nii.gz",
+                    # CSF MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "CSF_probseg.nii.gz"
                     ),
+                    # GM native
+                    f"anat/{t_sub}_label-GM_probseg.nii.gz",
+                    # GM MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "GM_probseg.nii.gz"
                     ),
+                    # WM native
+                    f"anat/{t_sub}_label-WM_probseg.nii.gz",
+                    # WM MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "WM_probseg.nii.gz"
                     ),
+                    # BOLD native
+                    (
+                        f"func/{t_sub}_task-moviewatching_space-"
+                        "T1w_desc-preproc_bold.nii.gz"
+                    ),
+                    # BOLD MNI152NLin2009cAsym
                     (
                         f"func/{t_sub}_task-moviewatching_space-"
                         "MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                     ),
+                    # BOLD brain mask native
+                    (
+                        f"func/{t_sub}_task-moviewatching_"
+                        "space-T1w_desc-brain_mask.nii.gz"
+                    ),
+                    # BOLD brain mask MNI152NLin2009cAsym
+                    (
+                        f"func/{t_sub}_task-moviewatching_"
+                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                    ),
+                    (
+                        f"func/{t_sub}_task-moviewatching_space-"
+                        "T1w_desc-preproc_bold.json"
+                    ),
                     (
                         f"func/{t_sub}_task-moviewatching_space-"
                         "MNI152NLin2009cAsym_desc-preproc_bold.json"
                     ),
+                    # BOLD confounds
                     (
                         f"func/{t_sub}_task-moviewatching_desc-confounds"
                         "_regressors.tsv"
@@ -71,13 +112,15 @@ with TemporaryDirectory() as tmpdir_name:
                         f"func/{t_sub}_task-moviewatching_desc-confounds"
                         "_regressors.json"
                     ),
+                    # BOLD reference native
                     (
                         f"func/{t_sub}_task-moviewatching_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                        "space-T1w_boldref.nii.gz"
                     ),
+                    # BOLD reference MNI152NLin2009cAsym
                     (
-                        f"anat/{t_sub}_space-MNI152NLin2009cAsym_"
+                        f"func/{t_sub}_task-moviewatching_"
-                        "desc-brain_mask.nii.gz"
+                        "space-MNI152NLin2009cAsym_boldref.nii.gz"
                     ),
                 ]
 

tools/create_aomicpiop1_example_dataset.py

@@ -5,6 +5,7 @@
 #          Xuan Li <xu.li@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
+
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -35,22 +36,37 @@ with TemporaryDirectory() as tmpdir_name:
                     (sub_dir / dname).mkdir()
 
                 fnames = [
+                    # T1w native
+                    f"anat/{t_sub}_desc-preproc_T1w.nii.gz",
+                    # T1w MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_desc-preproc"
                         "_T1w.nii.gz"
                     ),
+                    # T1w brain mask native
+                    f"anat/{t_sub}_desc-brain_mask.nii.gz",
+                    # T1w brain mask MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_"
                         "desc-brain_mask.nii.gz"
                     ),
+                    # CSF native
+                    f"anat/{t_sub}_label-CSF_probseg.nii.gz",
+                    # CSF MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "CSF_probseg.nii.gz"
                     ),
+                    # GM native
+                    f"anat/{t_sub}_label-GM_probseg.nii.gz",
+                    # GM MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "GM_probseg.nii.gz"
                     ),
+                    # WM native
+                    f"anat/{t_sub}_label-WM_probseg.nii.gz",
+                    # WM MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "WM_probseg.nii.gz"
@@ -66,18 +82,35 @@ with TemporaryDirectory() as tmpdir_name:
                     "workingmemory_acq-seq",
                 ]
                 for t in tasks:
+                    # BOLD native
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_space-"
+                        "T1w_desc-preproc_bold.nii.gz"
+                    )
+                    # BOLD MNI152NLin2009cAsym
                     fnames.append(
                         f"func/{t_sub}_task-{t}_space-"
                         "MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                     )
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_space-"
+                        "T1w_desc-preproc_bold.json"
+                    )
                     fnames.append(
                         f"func/{t_sub}_task-{t}_space-"
                         "MNI152NLin2009cAsym_desc-preproc_bold.json"
                     )
+                    # BOLD brain mask native
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_space-"
+                        "T1w_desc-brain_mask.nii.gz"
+                    )
+                    # BOLD brain mask MNI152NLin2009cAsym
                     fnames.append(
                         f"func/{t_sub}_task-{t}_space-"
                         "MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
                     )
+                    # BOLD confounds
                     fnames.append(
                         f"func/{t_sub}_task-{t}_desc-confounds"
                         "_regressors.tsv"
@@ -86,6 +119,15 @@ with TemporaryDirectory() as tmpdir_name:
                         f"func/{t_sub}_task-{t}_desc-confounds"
                         "_regressors.json"
                     )
+                    # BOLD reference native
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_" "space-T1w_boldref.nii.gz"
+                    )
+                    # BOLD reference MNI152NLin2009cAsym
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_"
+                        "space-MNI152NLin2009cAsym_boldref.nii.gz"
+                    )
 
             elif dtype == "dwipreproc":
                 dname = "dwi"

tools/create_aomicpiop2_example_dataset.py

@@ -5,6 +5,7 @@
 #          Xuan Li <xu.li@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
+
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -35,22 +36,37 @@ with TemporaryDirectory() as tmpdir_name:
                     (sub_dir / dname).mkdir()
 
                 fnames = [
+                    # T1w native
+                    f"anat/{t_sub}_desc-preproc_T1w.nii.gz",
+                    # T1w MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_desc-preproc"
                         "_T1w.nii.gz"
                     ),
+                    # T1w brain mask native
+                    f"anat/{t_sub}_desc-brain_mask.nii.gz",
+                    # T1w brain mask MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym"
                         "_desc-brain_mask.nii.gz"
                     ),
+                    # CSF native
+                    f"anat/{t_sub}_label-CSF_probseg.nii.gz",
+                    # CSF MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "CSF_probseg.nii.gz"
                     ),
+                    # GM native
+                    f"anat/{t_sub}_label-GM_probseg.nii.gz",
+                    # GM MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "GM_probseg.nii.gz"
                     ),
+                    # WM native
+                    f"anat/{t_sub}_label-WM_probseg.nii.gz",
+                    # WM MNI152NLin2009cAsym
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"
                         "WM_probseg.nii.gz"
@@ -64,18 +80,35 @@ with TemporaryDirectory() as tmpdir_name:
                     "workingmemory_acq-seq",
                 ]
                 for t in tasks:
+                    # BOLD native
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_space-"
+                        "T1w_desc-preproc_bold.nii.gz"
+                    )
+                    # BOLD MNI152NLin2009cAsym
                     fnames.append(
                         f"func/{t_sub}_task-{t}_space-"
                         "MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                     )
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_space-"
+                        "T1w_desc-preproc_bold.json"
+                    )
                     fnames.append(
                         f"func/{t_sub}_task-{t}_space-"
                         "MNI152NLin2009cAsym_desc-preproc_bold.json"
                     )
+                    # BOLD brain mask native
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_space-"
+                        "T1w_desc-brain_mask.nii.gz"
+                    )
+                    # BOLD brain mask MNI152NLin2009cAsym
                     fnames.append(
                         f"func/{t_sub}_task-{t}_space-"
                         "MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
                     )
+                    # BOLD confounds
                     fnames.append(
                         f"func/{t_sub}_task-{t}_desc-confounds"
                         "_regressors.tsv"
@@ -84,6 +117,15 @@ with TemporaryDirectory() as tmpdir_name:
                         f"func/{t_sub}_task-{t}_desc-confounds"
                         "_regressors.json"
                     )
+                    # BOLD reference native
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_" "space-T1w_boldref.nii.gz"
+                    )
+                    # BOLD reference MNI152NLin2009cAsym
+                    fnames.append(
+                        f"func/{t_sub}_task-{t}_"
+                        "space-MNI152NLin2009cAsym_boldref.nii.gz"
+                    )
 
             elif dtype == "dwipreproc":
                 dname = "dwi"